Please wait a minute...
Journal of Integrative Agriculture  2021, Vol. 20 Issue (7): 1898-1906    DOI: 10.1016/S2095-3119(20)63488-8
Special Issue: 动物科学合辑Animal Science
Animal Science · Veterinary Medicine Advanced Online Publication | Current Issue | Archive | Adv Search |
Genome-wide scan for selection signatures based on whole-genome re-sequencing in Landrace and Yorkshire pigs
WANG Kai1*, WU Ping-xian1*, CHEN De-juan1, ZHOU Jie1, YANG Xi-di1, JIANG An-an1, MA Ji-deng1, TANG Qian-zi1, XIAO Wei-hang1, JIANG Yan-zhi2, ZHU Li1, QIU Xiao-tian3, LI Ming-zhou1, LI Xue-wei1, TANG Guo-qing1 
1 Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R.China
2 College of Life Science, Sichuan Agricultural University, Ya’an 625014, P.R.China
3 National Animal Husbandry Service, Beijing 100125, P.R.China
Download:  PDF in ScienceDirect  
Export:  BibTeX | EndNote (RIS)      

长白猪和大白猪是重要的商品猪品种。在长期的育种过程中,由于两种猪的育种目标不同,经过强烈的人工选择,长白猪和大白猪在猪基因组上有不同的选择信号,这些选择信号反映了它们特定的表型特征。因此本研究旨在通过全基因组选择信号扫描检测长白猪和大白猪之间的选择痕迹差异,从而为长白猪和大白猪的育种历史提供基础数据支持。在本研究中我们使用了Z转换的FST(Z(FST))和Z转换的杂合度(ZHp)两种方法对长白猪和大白猪进行全基因组扫描。在扫描过程中我们使用滑动窗口(40-kb窗口和20-kb步长)来检验FST值和杂合度,然后对FST值和杂合度进行Z转换,当滑动窗口的Z(FST)>5或ZHp<-2.8时,我们将该窗口确定为显著窗口,然后基于该窗口的基因组范围搜索候选基因。我们使用Z(FST)的方法找到了17个显著窗口,基于这些窗口找到15个注释元件,其中包括13个基因,比如UGP2基因, RAB3C基因和TLL1基因;我们使用ZHp的方法鉴别了363个显著窗口,基于这些窗口找到208个注释元件,其中包括140个基因,比如PPP3CA基因,PTPN13基因和MAPK10基因。功能分析和相关研究结果表明,大部分候选基因与基础代谢、抗病、细胞过程和生化信号有关,有几个与机体形态和器官有关。研究结果表明由于长期的人工选择,长白猪和大白猪在猪基因组上有明显不同的选择足迹。本研究基于全基因组重测序数据对长白猪和大白猪进行全基因组选择信号扫描,与其他研究相比,我们鉴别出了两个品种特定的差异基因组区域和候选基因,这些结果可以帮助研究者更好的了解人工选择对长白猪和大白猪的选择作用以及为这两个品种的现代育种提供新的方向。

We performed a genome-wide scan to detect selection signatures that showed evidence of positive selection in the domestication process by re-sequencing the whole genomes of Landrace and Yorkshire pigs.  Fifteen annotated elements with 13 associated genes were identified using the Z-transformed FST (Z(FST)) method, and 208 annotated elements with 140 associated genes were identified using the Z-transformed heterozygosity (ZHp) method.  The functional analysis and the results of previous studies showed that most of the candidate genes were associated with basic metabolism, disease resistance, cellular processes, and biochemical signals, and several were related to body morphology and organs.  They included PPP3CA, which plays an essential role in the transduction of intracellular Ca2+-mediated signals, and WWTR1, which plays a pivotal role in organ size control and tumor suppression.  These results suggest that genes associated with body morphology were subject to selection pressure during domestication, whereas genes involved in basic metabolism and disease resistance were subject to selection during artificial breeding.  Our findings provide new insights into the potential genetic variation of phenotypic diversity in different pig breeds and will help to better understand the selection effects of modern breeding in Landrace and Yorkshire pigs.
Keywords:  pig        variation        whole-genome sequence        selection signature        phenotypic trait  
Received: 14 May 2020   Accepted:
Fund: The study was supported by the grants from the Sichuan Science and Technology Program, China (2020YFN0024), the earmarked fund for the China Agriculture Research System (CARS-35-01A), the National Key R&D Program of China (2018YFD0501204), the National Natural Science Foundation of China (C170102), and the Sichuan Innovation Team of Pig, China (sccxtd-2021-08).
Corresponding Authors:  Correspondence TANG Guo-qing, E-mail:,    
About author:  WANG Kai, E-mail:; * These authors contributed equally to this study.

Cite this article: 

WANG Kai, WU Ping-xian, CHEN De-juan, ZHOU Jie, YANG Xi-di, JIANG An-an, MA Ji-deng, TANG Qian-zi, XIAO Wei-hang, JIANG Yan-zhi, ZHU Li, QIU Xiao-tian, LI Ming-zhou, LI Xue-wei, TANG Guo-qing. 2021. Genome-wide scan for selection signatures based on whole-genome re-sequencing in Landrace and Yorkshire pigs. Journal of Integrative Agriculture, 20(7): 1898-1906.

Andersson L, Georges M. 2004. Domestic-animal genomics: Deciphering the genetics of complex traits. Nature Reviews Genetics, 5, 202–212.
Van der Auwera G A, Carneiro M O, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, Jordan T, Shakir K, Roazen D, Thibault J. 2013. From FastQ data to high-confidence variant calls: The genome analysis toolkit best practices pipeline. Current Protocols in Bioinformatics, 43, doi: 10.1002/0471250953.bi1110s43.
Bandelt H J, Forster P, Röhl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16, 37–48.
Cingolani P, Platts A, Wang L L, Coon M, Nguyen T, Wang L, Land S J, Lu X, Ruden D M. 2012. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly, 6, 80–92.
Clark T G, Conway S J, Scott I C, Labosky P A, Winnier G, Bundy J, Hogan B L, Greenspan D S. 1999. The mammalian Tolloid-like 1 gene, Tll1, is necessary for normal septation and positioning of the heart. Development, 126, 2631.
Danecek P, Auton A, Abecasis G, Albers C A, Banks E, DePristo M A, Handsaker R E, Lunter G, Marth G T, Sherry S T. 2011. The variant call format and VCFtools. Bioinformatics, 27, 2156–2158.
Darwin C. 2010. The Variation of Animals and Plants Under Domestication. vol. 2. Cambridge University Press, London, UK.
Davoli R, Luise D, Mingazzini V, Zambonelli P, Russo V. 2015. Genome-wide study on intramuscular fat in Italian Large White pig breed using the PorcineSNP60 BeadChip. Journal of Animal Breeding & Genetics, 133, 277–282.
Evin A, Dobney K, Schafberg R, Owen J, Vidarsdottir U S, Larson G, Cucchi T. 2015. Phenotype and animal domestication: A study of dental variation between domestic, wild, captive, hybrid and insular Sus scrofa. BMC Evolutionary Biology, 15, 6.
Evin A, Owen J, Larson G, Debiais-Thibaud M, Cucchi T, Vidarsdottir U S, Dobney K. 2017. A test for paedomorphism in domestic pig cranial morphology. Biology Letters, 13, 20170321.
Felsenstein J. 2004. PHYLIP (phylogeny inference package) version 3.6. distributed by the author. [2018-03-19].
Giuffra E, Kijas J M, Amarger V, Carlborg O, Jeon J T, Andersson L. 2000. The origin of the domestic pig: Independent domestication and subsequent introgression. Genetics, 154, 1785.
Groenen M A M, Archibald A L, Uenishi H, Tuggle C K, Takeuchi Y, Rothschild M F, Rogelgaillard C, Park C, Milan D, Megens H J. 2012. Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 491, 393–398.
Kinsella R J, Kähäri A, Haider S, Zamora J, Proctor G, Spudich G, Almeidaking J, Staines D, Derwent P, Kerhornou A. 2011. Ensembl biomarts: A hub for data retrieval across taxonomic space. Database, 2011, bar030.
Larson G, Albarella U, Dobney K, Rowleyconwy P, Schibler J, Tresset A, Vigne J D, Edwards C J, Schlumbaum A, Dinu A. 2007. Ancient DNA, pig domestication, and the spread of the Neolithic into Europe. Proceedings of the National Academy of Sciences of the United States of America, 104, 15276–15281.
Larson G, Dobney K, Albarella U, Fang M, Matisoosmith E, Robins J, Lowden S, Finlayson H, Brand T, Willerslev E. 2005. Worldwide phylogeography of wild boar reveals multiple centers of pig domestication. Science, 307, 1618–1621.
Lee W, Taye M, Kwon T, Yoon J, Jang D, Suzuki S, Kim H. 2017. Identifying candidate positive selection genes in Korean imported pig breeds. Genes & Genomics, 39, 557–565.
Li H, Durbin R. 2009a. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25, 1754–1760.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009b. The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078–2079.
Ma Y, Wei J, Zhang Q, Chen L, Wang J, Liu J, Ding X. 2015. A genome scan for selection signatures in pigs. PLoS ONE, 10, e0116850.
Mason I L. 1984. Evolution of Domesticated Animals. Longman, London, UK.
Moon S, Kim T H, Lee K T, Kwak W, Lee T, Lee S W, Kim M J, Cho K, Kim N, Chung W H. 2015. A genome-wide scan for signatures of directional selection in domesticated pigs. BMC Genomics, 16, 1–12.
Nielsen R. 2005. Molecular signatures of natural selection. Annual Review of Genetics, 39, 197–218.
Peng H L, Chang H Y. 1993. Cloning of a human liver UDP-glucose pyrophosphorylase cDNA by complementation of the bacterial galU mutation. Febs Letters, 329, 153.
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira M A R, Bender D, Maller J, Sklar P, de Bakker P I W, Daly M J, Sham PC. 2007. PLINK: A tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics, 81, 559–575.
Rubin C J, Megens H J, Barrio A M, Maqbool K, Andersson L. 2012. Strong signatures of selection in the domestic pig genome. Proceedings of the National Academy of Sciences of the United States of America, 109, 19529–19536.
Wang K, Wu P, Yang Q, Chen D, Zhou J, Jiang A, Ma J, Tang Q, Xiao W, Jiang Y. 2018. Detection of selection signatures in Chinese landrace and yorkshire pigs based on genotyping-by-sequencing data. Frontiers in Genetics, 9, 119.
Wang Z, Chen Q, Yang Y, Yang H, He P, Zhang Z, Chen Z, Liao R, Tu Y, Zhang X. 2014. A genome-wide scan for selection signatures in Yorkshire and Landrace pigs based on sequencing data. Animal Genetics, 45, 808–816.
Wilkinson S, Lu Z H, Megens H J, Archibald A L, Haley C, Jackson I J, Groenen M A, Crooijmans R P, Ogden R, Wiener P. 2013. Signatures of diversifying selection in European pig breeds. PLoS Genetics, 9, e1003453.
Yang J, Lee S H, Goddard M E, Visscher P M. 2011. GCTA: A tool for genome-wide complex trait analysis. The American Journal of Human Genetics, 88, 76–82.
Yang S, Li X, Li K, Fan B, Tang Z. 2014. A genome-wide scan for signatures of selection in Chinese indigenous and commercial pig breeds. BMC Genetics, 15, 7.
Yu J Y, Shao S M, Chen K, Lei M G, Xiong Y Z. 2014. Expression patterns and promoter activity analysis of UGP2 in pigs. Genetics & Molecular Research Gmr, 13, 1358–1365.
Zhu Y, Li W, Yang B, Zhang Z, Huang L. 2017. Signatures of selection and interspecies introgression in the genome of Chinese domestic pigs. Genome Biology & Evolution, 9, 2592–2603.
[1] XU Kui, ZHOU Yan-rong, SHANG Hai-tao, XU Chang-jiang, TAO Ran, HAO Wan-jun, LIU Sha-sha, MU Yu-lian, XIAO Shao-bo, LI Kui. Pig macrophages with site-specific edited CD163 decrease the susceptibility to infection with porcine reproductive and respiratory syndrome virus[J]. >Journal of Integrative Agriculture, 2023, 22(7): 2188-2199.
[2] LIAO Zhen-qi, DAI Yu-long, WANG Han, Quirine M. KETTERINGS, LU Jun-sheng, ZHANG Fu-cang, LI Zhi-jun, FAN Jun-liang. A double-layer model for improving the estimation of wheat canopy nitrogen content from unmanned aerial vehicle multispectral imagery[J]. >Journal of Integrative Agriculture, 2023, 22(7): 2248-2270.
[3] XIE Lei, QIN Jiang-tao, RAO Lin, CUI Deng-shuai, TANG Xi, XIAO Shi-jun, ZHANG Zhi-yan, HUANG Lu-sheng. Effects of carcass weight, sex and breed composition on meat cuts and carcass trait in finishing pigs[J]. >Journal of Integrative Agriculture, 2023, 22(5): 1489-1501.
[4] XIANG Guang-ming, ZHANG Xiu-ling, XU Chang-jiang, FAN Zi-yao, XU Kui, WANG Nan, WANG Yue, CHE Jing-jing, XU Song-song, MU Yu-lian, LI Kui, LIU Zhi-guo. The collagen type I alpha 1 chain gene is an alternative safe harbor locus in the porcine genome[J]. >Journal of Integrative Agriculture, 2023, 22(1): 202-213.
[5] LONG Ke-ren, LI Xiao-kai, ZHANG Ruo-wei, GU Yi-ren, DU Min-jie, XING Xiang-yang, DU Jia-xiang, MAI Miao-miao, WANG Jing, JIN Long, TANG Qian-zi, HU Si-lu, MA Ji-deng, WANG Xun, PAN Deng-ke, LI Ming-zhou. Transcriptomic analysis elucidates the enhanced skeletal muscle mass, reduced fat accumulation, and metabolically benign liver in human follistatin-344 transgenic pigs[J]. >Journal of Integrative Agriculture, 2022, 21(9): 2675-2690.
[6] WANG Kai, WU Ping-xian, WANG Shu-jie, JI Xiang, CHEN Dong, JIANG An-an, XIAO Wei-hang, JIANG Yan-zhi, ZHU Li, ZENG Yang-shuang, XU Xu, QIU Xiao-tian, LI Ming-zhou, LI Xue-wei, TANG Guo-qing. Epigenome-wide DNA methylation analysis reveals differentially methylation patterns in skeletal muscle between Chinese Chenghua and Qingyu pigs[J]. >Journal of Integrative Agriculture, 2022, 21(6): 1731-1739.
[7] WANG Peng-fei, WANG Ming, SHI Zhi-bin, SUN Zhen-zhao, WEI Li-li, LIU Zai-si, WANG Shi-da, HE Xi-jun, WANG Jing-fei. Development of a recombinant pB602L-based indirect ELISA assay for detecting antibodies against African swine fever virus in pigs[J]. >Journal of Integrative Agriculture, 2022, 21(3): 819-825.
[8] TONG Shi-feng, ZHU Mo , XIE Rui , LI Dong-feng , ZHANG Li-fan , LIU Yang.

Genome-wide detection for runs of homozygosity analysis in three pig breeds from Chinese Taihu Basin and Landrace pigs by SLAF-seq data [J]. >Journal of Integrative Agriculture, 2022, 21(11): 3293-3301.

[9] QIAN Li-li, XIE Jing-yi, GAO Ting, CAI Chun-bo, JIANG Sheng-wang, BI Han-fang, XIE Shan-shan, CUI Wen-tao. Targeted myostatin loss-of-function mutation increases type II muscle fibers in Meishan pigs[J]. >Journal of Integrative Agriculture, 2022, 21(1): 188-198.
[10] WU Ping-xian, ZHOU Jie, WANG Kai, CHEN De-juan, YANG Xi-di, LIU Yi-hui, JIANG An-an, SHEN Lin-yuan, JIN Long, XIAO Wei-hang, JIANG Yan-zhi, LI Ming-zhou, ZHU Li, ZENG Yang-shuang, XU Xu, QIU Xiao-tian, LI Xue-wei, TANG Guo-qing. Identifying SNPs associated with birth weight and days to 100 kg traits in Yorkshire pigs based on genotyping-by-sequencing[J]. >Journal of Integrative Agriculture, 2021, 20(9): 2483-2490.
[11] SUN Hui-li, WANG Xin-yue, SHANG Ye, WANG Xiao-qian, DU Guo-dong, LÜ De-guo. Preharvest application of melatonin induces anthocyanin accumulation and related gene upregulation in red pear (Pyrus ussuriensis)[J]. >Journal of Integrative Agriculture, 2021, 20(8): 2126-2137.
[12] ZHANG Zhe, CHEN Zi-tao, DIAO Shu-qi, YE Shao-pan, WANG Jia-ying, GAO Ning, YUAN Xiao-long, CHEN Zan-mou, ZHANG Hao, LI Jia-qi. Identifying the complex genetic architecture of growth and fatness traits in a Duroc pig population[J]. >Journal of Integrative Agriculture, 2021, 20(6): 1607-1614.
[13] WANG Xiao-bo, WU Nan, CAI Rui-jie, GENG Wei-na, XU Xiao-yan. Changes in speciation, mobility and bioavailability of Cd, Cr and As during the transformation process of pig manure by black soldier fly larvae (Hermetia illucens)[J]. >Journal of Integrative Agriculture, 2021, 20(5): 1157-1166.
[14] DIAO Shu-qi, XU Zhi-ting, YE Shao-pan, HUANG Shu-wen, TENG Jin-yan, YUAN Xiao-long, CHEN Zan-mou, ZHANG Hao, LI Jia-qi, ZHANG Zhe. Exploring the genetic features and signatures of selection in South China indigenous pigs[J]. >Journal of Integrative Agriculture, 2021, 20(5): 1359-1371.
[15] ZHU Mei-chen, HU Ran, ZHAO Hui-yan, TANG Yun-shan, SHI Xiang-tian, JIANG Hai-yan, ZHANG Zhi-yuan, FU Fu-you, XU Xin-fu, TANG Zhang-lin, LIU Lie-zhao, LU Kun, LI Jia-na, QU Cun-min. Identification of quantitative trait loci and candidate genes controlling seed pigments of rapeseed[J]. >Journal of Integrative Agriculture, 2021, 20(11): 2862-2879.
No Suggested Reading articles found!